Variant report

Variant	rs2518112
Chromosome Location	chr9:108288060-108288061
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10115299	0.86[EUR][1000 genomes]
rs10761100	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10816278	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10820809	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10820810	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10820812	0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[ASN][1000 genomes]
rs10820813	0.96[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1327354	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs1360089	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1806898	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1815383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1960023	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1987634	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2225246	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2427769	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2518106	0.91[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2518114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518116	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2518120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2518123	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2518124	0.93[ASN][1000 genomes]
rs2518128	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs2518131	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2768279	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs2768280	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2768283	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2768290	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2768291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2768292	0.93[ASN][1000 genomes]
rs2768294	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2771038	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2771041	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2771042	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2812297	0.84[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.80[ASN][1000 genomes]
rs2812303	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2812307	0.92[ASN][1000 genomes]
rs2812308	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2812310	0.92[ASW][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4742650	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4742947	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4742948	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477447	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6477449	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7020083	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7357632	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs7864020	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv893692	chr9:108218852-108320988	ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
4	nsv1050141	chr9:108219667-108317424	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
5	nsv982334	chr9:108282762-108289464	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
2	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
3	chr9:108231800-108296800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:108242600-108300000	Weak transcription	Brain Anterior Caudate	brain
5	chr9:108268200-108306000	Weak transcription	Brain Angular Gyrus	brain
6	chr9:108272800-108304600	Weak transcription	NHEK	skin
7	chr9:108274400-108299800	Weak transcription	Fetal Lung	lung
8	chr9:108276200-108309200	Weak transcription	Lung	lung
9	chr9:108278000-108292800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:108278800-108296600	Weak transcription	A549	lung
11	chr9:108278800-108297000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:108278800-108305800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr9:108279000-108290000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:108279000-108293200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr9:108279000-108296000	Weak transcription	Fetal Muscle Leg	muscle
16	chr9:108279000-108311400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr9:108279000-108317600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:108279200-108297400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:108279200-108313000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr9:108279400-108296800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:108279600-108294800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:108279600-108296800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:108280200-108289600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:108280200-108289800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:108280200-108297200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr9:108282400-108288400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr9:108282400-108289800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr9:108282400-108290400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:108282400-108292200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:108282400-108293200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:108282400-108294200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:108282400-108294800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr9:108282400-108294800	Weak transcription	NH-A	brain
34	chr9:108282400-108296400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr9:108282400-108296800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr9:108282400-108296800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:108282400-108297600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr9:108282400-108299600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr9:108282400-108300000	Weak transcription	HSMMtube	muscle
40	chr9:108282400-108302800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:108282400-108302800	Weak transcription	HSMM	muscle
42	chr9:108282400-108312400	Weak transcription	HepG2	liver
43	chr9:108282400-108319800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr9:108282400-108319800	Weak transcription	Left Ventricle	heart
45	chr9:108282400-108319800	Weak transcription	Psoas Muscle	Psoas
46	chr9:108282600-108319800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:108285200-108296800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr9:108285400-108288200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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